We propose to generate comprehensive nonhuman primate (NHP) reference transcriptome databases using lllumina's next-generation sequencing platform. These databases will contain information on protein-coding, long noncoding, and small noncoding transcripts, and will provide vast amounts of new information regarding gene and transcript structure, expression, and regulation. To enhance this resource, we will also generate a tissue-specific transcriptome atlas for rhesus macaque and whole transcriptome information from a NHP model of AIDS. These databases will serve as a resource for scientists working on evolution, comparative biology, genetics, genomics, and NHP models of human disease. In Aim 1, we will collaborate with lllumina scientists to generate whole transcriptome (protein-coding and long noncoding) information for 14 NHP species/subspecies, lllumina will perform this sequencing at no cost to the application. The majority of these NHP genomes will be sequenced within the year, and transcriptome information will facilitate genome assembly, annotation, development of new tools for systems biology research, while also providing broad resources for evolutionary biologists. To complement the whole transcriptome project, we will use our lllumina Genome Analyzer to generate a tissue specific transcriptome for rhesus macaque, the most widely used NHP in biomedical research. In Aim 2, we will sequence protein-coding, long noncoding, and small noncoding transcripts from an independently funded study focused on a NHP acute infection model of AIDS. The resulting data will expand the NHP reference transcriptome databases to include new information on virus-host interactions, innate immunity, inflammatory processes, the transition to the adaptive immune response, and infection-induced transcripts. Finally, whole transcriptome data from both Aims will enable the discovery and quantification of noncoding RNAs, which have widespread functionality but are not well understood. Given the importance of NHP primates as models for human health and disease, it is imperative that whole transcriptome information be available for these animals.